Environmental pollution from diesel ship is very serious. To reduce pollution, we consider fuel cell which can replace diesel engine. For small boat, fuel cell can operate main power and for large vessel, it can use auxiliary power unit. Desulfurize system is very important for using fuel cell, because sulfur compuund influence catalyst poison around low concentration, 1 ppm. So in this study, we performed diesel desulfurization reactor design by numerical analysis. This study is divided four step. The first step is basic reactor design. By analyzing the change in flow and sulfur concentration at the outlet according to the changes in flow rate, reactor length, and reactor diameter, we have found the minimum catalyst performance for the given flow rate condition and the relation between the reactor performance and the reactor size and shape. We analyzed the changes in regeneration process according to purge gas flow rate, catalyst permeability, reactor size, and heat loss of reactor. We also estimated the regeneration time according to purge gas flow rate and initial temperatures and have found that increasing purge gas temperature is more effect for fast regeneration. The second step is reacor scale up and oprating optimization. Using experimental results and the adsorption kinetics theory, the adsorption rate of sulfur in diesel was estimated and verified by numerical analysis. By analyzing the performance of desulfurization according to reactor size, the optimal reactor size was determined. Through maximization of processed diesel amount, optimal diesel flow rate was determined. Regeneration process was also confirmed for the obtained optimal reactor size. At the third step, designed process simulation of 100 kW fuel cell system and desulfurize module for adapting fuel cell system. In this step, we operate the HYSYS for modeling process simulation as well as numerical analysis. For desulfurizing module, we performed modeling and optimization to prevent the poisoning effect. According to heat transfer analysis between desulfurize reactors, we check the distance influence from other reactors. In this results, Design change of reactor is not necessary, because recycling diesel is already desulfurized and it mixed. So, input concentration is reduced. To operating TSA process, we get the fluidity of process because less sulfur amount than adsorption capacity of sulfur is adsorbed by a reactor. Finally, heat interference of reactors is not occurred short distance of reactors. This results will be contribute the fuel cell system which can utilize new and renewable energy source, and desulfurize module design is contribute the basic of clean petrochemical technology besides fuel cell system.